Theory and Windows-based program to calculate mass spectra.

- Parameters of simulated annealing optimization can be set
- This version comes with 2 exe files: Masskinetics Scientific and Masskinetics Scientific Collision. The 'Collision' version runs about 100 times faster compared to the standard version. Unfortunately it has some limitations (e.g. radiative energy transfer, SID cannot be modelled), but it is capable to model the most important collisional energy transfer.
- Console version of MassKinetics Collisions 2.1 - it is without user interface, but runs even faster (requires a processor with AVX2 instruction set - practically it means Intel i3/i5/i7/i9/i11 and AMD Ryzen processors)
- If you find any error in the program, please contact me or send a bugreport.

- Model mass spectrometric processes and to calculate ion abundances
- Model collisional and radiative energy exchange (excitation/cooling)
- Provide connection between mass spectrometry & thermodynamics
- Study non-equilibrium reaction kinetics

- For teaching mass spectrometry, to demonstrate internal energy effects, create interest in MS using computer simulations
- For teaching and illustrating basic reaction kinetics

- Calculations require molecular parameters (experimental or theoretical), definition of experimental conditions and very few adjustable parameters. The results are very accurate (see references).
- The program is easy to use, runs under Windows

Theory

- L. Drahos and K. Vékey,
*J. Mass Spectrom.***36**, 237 (2001) (This paper describes the theory of MassKinetics)

Applications

- L. Drahos, R. M. A. Heeren, C. Collette, E. D. Pauw and K. Vékey,
*J. Mass Spectrom***34**, 1373 (1999) (MassKinetics was used to determine the shape of internal energy distribution of ions formed in an electrospray ion source) - L. Drahos and K. Vékey,
*J. Mass Spectrom.***34**, 79-84 (1999) (A study of the role of effective temperature in the kinetic method using MassKinetics) - L. Drahos and K. Vékey,
*J. Am. Soc. Mass Spectrom.***10**, 323-328 (1999) (An application to determine thermal internal energies and internal energy distributions using an early version of MassKinetics) - P. D. Thomas, R. G. Cooks, K. Vékey, L. Drahos and C. Wesdemiotis,
*J. Phys. Chem. A***104**, 1359-1361 (2000) (Calculation of the kinetic method plot using MassKinetics for several alcohols based on molecular parameters, and comparing the results to experimental data determined by Holmes et al.) - L. Wua, J. W. Denault, R.G. Cooks, L. Drahos and K. Vékey,
*J. Am. Soc. Mass Spectrom.*,**13**, 1386-1393 (2002) (Modeling CID fragmentation of NaClRb^{+}cluster ion: Calculation of effective temperature and survival yield as a function of collisional energy transfer and pressure of collision gas) - Z. Takáts, L. Drahos, G. Schlosser and K. Vékey, Anal. Chem, 74(24); 6427-6429 (2002): Feasibility of Formation of Hot Ions in Electrospray (Modeling the effect of collisional cooling using different collision gases)
- László Drahos, Judit Sztáray and Károly Vékey, International Journal of Mass Spectrometry, In Press, Theoretical calculation of isotope effects, kinetic energy release and effective temperatures for alkylamines

.

Modeling CID fragmentation of NaClRb^{+} cluster

The details of this example can be found in the following article: L. Wua, J. W. Denault, R.G. Cooks, L. Drahos and K. Vékey, *J. Am. Soc. Mass Spectrom*, **13**, 1386-1393 (2002)

Calculated (B3-LYP/SDD basis set) vibrational frequencies (cm^{-1}) of [Na-Cl-Rb]^{+}: 56.6447, 56.6456, 133.5272, 324.7957.

Click here to download this MassKinetics frequency file.

**Fig. 3a:**MassKinetic calculated survival yield vs. collision efficiency curve of [Na-Cl-Rb]^{+} under single collision conditions.

**Fig. 3b: **MassKinetic calculated effective temperature T_{eff} vs. collision efficiency curve of [Na-Cl-Rb]^{+} under single collision conditions.

Click here to download this MassKinetics project file.

**Fig. 4a:** MassKinetic calculated survival yield vs. collision gas pressure (Pa) graph.

**Fig. 3b: **MassKinetic calculated effective temperature T_{eff} vs. collision gas pressure graph.

.

Modeling collisional cooling of p-methoxy-benyzlpyridinium ion colliding with Ar, N_{2} and isobutane gases

The details of this example can be found in the following article: (Z. Takáts, L. Drahos, G. Schlosser and K. Vékey, Is Formation of Hot Ions Feasible in Electrospray?, *Anal. Chem.* in press

Calculated (B3-LYP/6-31G(d,p)) vibrational frequencies (cm^{-1}) of p-methoxy-benyzlpyridinium ion: click here to download this MassKinetics frequency file.

Collisional cooling can be modeled reasonably well assuming long-lived collision complexes. In such a case the total energy of the two collision partners (the internal energy of the two partners and their relative rotational and translational energy) is distributed statistically between the various degrees of freedom. This process has been studied by MassKinetics model calculations. Preliminary results are shown in this figure illustrating the change of mean internal energy as a function of the number of collisions. Calculations were performed for p-methoxy-benyzlpyridinium ion colliding with Ar, N_{2} and isobutane collision gases. The model calculations clearly show, that isobutane is the best cooling medium, and that the difference between Ar and N_{2} is much less than that between N_{2} and isobutane. The cooling rates shown here. agree very well with the experimentally observed difference between these curtain gases.

The corresponding MassKinetics project file will be available when MassKinetics Scientific version is released.

.

**Modeling kinetic isotope effect
(KIE), effective temperature (T _{eff}) and kinetic energy release (KER)
of selected protonated alkylamine dimers**

**Welcome!**

We would like to give you a short introduction
to the modeling of the dissociation of protonated alkylamine dimers.

Various properties of the selected systems, such as kinetic
isotope effect, effective temperature and kinetic energy release can be
calculated using the following known parameters:

·
experimental setup (instrumental setup, lengths, source
temperature, acceleration voltages)

·
reaction enthalpy, vibrational frequencies for reactants and
products, preexponential factor for defining the transitional state

These
parameters can be found in the first window of each MassKintetics project file.

The
details of these calculations, the summarized results for all the tested system
and the conclusions can be found in the following article:

L. Drahos, J. Sztáray and K. Vékey *Int.
J. Mass Spectrom.*, **225** 233–248 (2003)

Also one can find excellent references for the kinetic method
that was used to get the interested data from the ion ratios and also for the
KER.

The theoretical background of the MassKinetics program can be
found in the following article:

L.
Drahos and K. Vékey* J. Mass Spectrom.*, **36**, 237-263 (2001)

**The types of calculations presented here:**

**1.
****Modeling KIE and T _{eff} **

**2.
****Modeling KER with calculating internal energy partitioning
and calculating the kinetics energy release distributions for the product ions**

**3.
****Modeling energy distributions: calculating the
internal energy distributions of the fragmenting parent ions and of the product
ions at different places.**

The required data for each of these
calculations as well as the parameters, which have been used in the modeling
can be found in the first page of the MassKinetics project file.

Two types of experiments were
modeled: using the high-pressure ion source (VG), and using the low-pressure
ion source (JEOL). One can find the MassKinetics project files for both
systems.

Also there were 11 protonated
alkylamine systems, which were modeled and presented in the referred article.
We would like to present here two systems of those: the smallest one and the
biggest one that is the protonated methyl-amin-methyld3-amin and the protonated
dietil-amin-dietil-d2-amin system. As for the example of the distributions
calculations we only dealt with the first, smallest system, so that is
presented here too.

**1. Modeling KIE and T _{eff} **

The kinetic isotope effect and the effective temperature can
be calculated of the interested system without calculating the internal energy
partitioning between the corresponding products. This means that only the
molecular ion and the two possible fragment ions are considered in the
modeling.

MassKinetics
project file for the *protonated methyl-amin-methyld3-amin* system using *high-pressure
ion source*:

Click here to download this
MassKinetics project file.

and
using *low-pressure ion source*:

Click here to
download this MassKinetics project file.

MassKinetics
project file for the *protonated diethyl-amin-diethyld2-amin* system using
*high-pressure ion source*:

Click here to
download this MassKinetics project file.

and
using *low-pressure ion source*:

Click here to
download this MassKinetics project file.

**2.
Modeling KER with calculating internal energy partitioning**

Calculating the kinetic energy release (KER) it is required
to calculate the internal energy partitioning over the products. It can be
selected in the *Molecular System/General *window in the MassKinetics
project file. Because calculating the internal energy partitioning involves the
neutral products also, one has to make a few changes comparing to the upper
project files. The *Reaction Scheme* should include the two possible
neutral products and these have to be considered in the *Reactions* window
too. Also the frequency model of the fragment ions has to be loaded in the M*olecular
System/Molecules* window and neutral products have to be loaded in the M*olecular
System/Reactions* window. The rest of the project file is very similar to
the upper ones.

MassKinetics
project file for the *protonated methyl-amin-methyld3-amin* system using *high-pressure
ion source*:

Click here to
download this MassKinetics project file.

and
using *low-pressure ion source*:

Click here to
download this MassKinetics project file.

MassKinetics
project file for the *protonated diethyl-amin-diethyld2-amin* system using
*high-pressure ion source*:

Click here to
download this MassKinetics project file.

and
using *low-pressure ion source*:

Click here to
download this MassKinetics project file.

And of course one can calculate the KER distribution for the
fragment ions. In order to do that you have to go to the *Results/Reaction (M**®**X)* window and select the 2D curve for
KER distribution. Here is an example for M*®*A dissociation.

Click here to
download this MassKinetics project file.

**3.
Modeling energy distributions**

Throughout
this section the low pressure ion source (JEOL instrument) setup will be used.

a,
Thermal energy distributions of the molecular ion

First let’s calculate the thermal internal energy
distributions for the molecular ions at selected temperature.

The temperature can be given at the *Molecular System/Molecules*
window by setting the internal energy of the molecular ion. The 2D curve has to
be selected at *Result/Reactant/Molecular Ion*. The presented project file
calculates the IED at 450K (internal energy of the molecular ion).

Click here to
download this MassKinetics project file.

b,
Internal energy distributions of the fragmenting ions at various place of the
mass spectrometer

In the referred article it is shown, that the molecular ions
can dissociate through two channels:
either the deuterated or the non-deuterated product ion can be formed.

It is interesting to check the difference in the internal
energy distributions of the two possible product ions.

MassKinetics project file for the *protonated methyld3-amin*
product ion using *low-pressure ion source*:

Click here to
download this MassKinetics project file.

MassKinetics
project file for the *protonated methyl-amin *product ion using *low-pressure
ion source*:

Click here to download
this MassKinetics project file.

Since there is only a minor difference in the distributions
of the two product ions, we decided to deal only with one of the two product
ions during the modeling of the energy distributions of the ions.

To set
the place where the energy distributions should be calculated it has to be
defined when the 2D curves are being selected. Here are three examples:

1.
Ions reaching the field free flight (FFR): this is right before the third
region

Click here to
download this MassKinetics project file.

2.
Ions leaving the field free flight (FFR): this is right after the third region

Click here to
download this MassKinetics project file.

3. Ions fragmenting in the field free region: in order to get
this distribution the difference between the first two distributions has to be
taken, that is the ions leaving the FFR and the ions reaching the FFR. So you
really don’t need a project file for doing this. J

**Hope you enjoy it!**

If you have any question or comment regarding the calculations or anything else, please don’t hesitate to ask us: szj@unc.edu or masskinetics@ttk.mta.hu

.

- MassKinetics Tutorial (modeling CID fragmentation (buthyl radical and buthene loss) of buthylbenzene on a sector type mass spectrometer)
- ion formation (pre-selected)
- electrostatic acceleration
- field free flight (through the 1
^{st}quad) - ion selection (of m/z 134)
- collision cascade/collision cell
- ion selection (through 3
^{rd}quad) followed by detection - How to use MassKinetics as a simple RRKM program

.

**MassKinetics Tutorial**

1. Introduction

Here we will show you in detail how to use the MassKinetics program in a simple case. In this tutorial various MassKinetics window names and menu items are printed ** red italic bold**; parameters to be selected by

We take the example published few years ago in a tutorial article in JMS on ion energetics (K. Vékey, J. Mass Spectrom. 31, 445-463 (1996)) – this is also a good place to start understanding fundamentals of mass spectrometry. First we show you how to set up a given experiment, next we show you how you can calculate various features for this model reaction. The ‘Tips and Tricks’ section of our homepage gives you ideas how to use MassKinetics for more advanced calculations. Tips for application of MassKinetics to chemical problems can be found in the ‘Examples’ and ‘References__’ __sections of this homepage.

Please note that we are in the process of developing and testing the program, and there are likely to be many errors and bugs in it. If you find one, please inform us, preferably sending us the project file ('mkp' extension) and a short explanation of the bug.

First, you have to start the program (by double clicking on its icon) and accept the license agreement. After that you get to the main window of MassKinetics:

If it is your first application, you have to create a new project (green arrow), otherwise you may open an existing one (red arrow). You may save your MassKinetics project any time, and you may change its name by "save as". In general, if you want to select or modify an item in the dialog box you have to click or double click on it – then you will either be able to type in the proper value, or you will be led to a new dialog box which you have to fill out properly.

If you want to learn, how to create a new MassKinetics project, continue with the next section. If you want to learn, how to modify an existing project and use it for various model calculations, go to the Tips & Tricks section.

2. Create a new project: *CID fragmentation (buthyl radical and buthene loss) of buthylbenzene*

After you create a new project (green arrow in the previous diagram) you will be able to click on the ** Setup** menu (blue arrow) to define your experiment. This brings up a dialog box and takes you to the "Comments" tab of this dialog:

In the ** Comments** window you can type (now, or any time later) comments about your MassKinetics project. To specify/modify the MassKinetics project, you have to go through

Here you select (red arrow) the required reaction type ("** parallel reaction**"). In future versions of MassKinetics you will have several more options, now you proceed to the

Here you define critical (~ activation) energy (** E0**, given in eV units) and the

You can characterize the ** Transition State** window using the pre-exponential (or frequency) factor. To do so, select the

In the table here you specify the molecular parameters and initial state of the compounds. The first column (red arrow) gives the ** name** of the ion – it is only for your information, and you can rename them as you wish by clicking on it and typing the new name. Rename Fragment A as ‘propene’, Fragment B as ‘propyl radical’. The second column (blue arrow) gives the molecular

In the "** Set Frequency Model**" dialog box you can specify the frequency model by clicking on the "

The MassKinetics Demo contains the ** frequency file** of buthylbenzene (Buthylbenzene.frq) in the MassKinetics folder, for other compounds you will have to prepare that in advance. The

The next column (red arrow) here is the initial concentration (** Conc**.) – at the time of ion formation the initial concentration of the molecular ion is unity, while it is zero for all other species (these are the default values). The

In the ** Internal Energy Distribution** window you can either specify a fixed, single value, or a thermal distribution. The latter is often a good approximation – the mean internal energy is defined using certain temperature. For buthylbenzene in EI ionization you may define internal energy distribution to correspond to 1000 K. You click on "

The last column in this dialog box (green arrow) is the initial kinetic energy (** Kin. Energy**), double clicking on it takes you to the

For the buthylbenzene example we do not consider radiative transitions, so leave the '** Radiative Energy Transfer (RET) is Considered'** checkbox (blue arrow) unchecked, which is the default. (Note that it is not necessary to open/close the Radiation dialog box, but it is worth checking, if it is correctly set. Proceed to the

In the collision window you can define collision parameters. The checkbox (red arrow) should be checked (default setting) to consider collisional energy transfer. In the right hand side you can define the ** name** and

This box defines the numerical accuracy of the calculations. You have to experiment with the various tolerance limits yourself. You can change the pre-set values by click/type. In most cases you can leave the ** Int. Energy Change**,

In the right hand side (red arrow) you have the possible experimental events (for a detailed description see L. Drahos and K. Vékey, *J. Mass Spectrom*. **36**, 237 (2001) ), on the left (blue arrow) your experimental setup. You can select one item by clicking on it. If you select one on the right hand side you can move it to the left column by clicking the ** Add** button. If you select one on the left, you can

EI ionization followed by CID in a typical triple quadrupole mass spectrometer can be defined using the following parameters: acceleration to 50 eV through 0.01 m distance, 0.50 m long distance to the collision region with selection of the molecular ion (1^{st} quad), 0.20 m long collision cell (2^{nd} quad), 0.50 m long distance through the 3^{rd} quad to the detector. In the collision region the pressure of the collision gas is ~ 0.05 Pa (ca. 0.5 torr).

To set up such an experiment select/** add** events in the following sequence:

When you have selected the proper experimental sequence, these will appear on the left hand side of this dialog box, as indicated in the figure above.

Now double-click on each item to define the specific parameters. Double-click on ** electrostatic acceleration**, which takes you to the following dialog box:

Here you should click on ** flight length**, and specify 0.01 (m); red arrow. Specify the

Now you click on ** flight length**, and specify 0.5 (m), and accept it (

You select the Molecular ion ‘buthilbenzene (M)’, accept it (** OK**), than continue with

Here you select ** flight length**, and specify 0.2 (m). Leave the

Here you have to check ** flight length**, set it to 0.5 (m) and accept it (

Here you specify ** single** calculation (blue arrow), and you can switch to the

Here you can specify what sort of data you want to obtain for results. Let’s assume that you want to know the concentration of the molecular and fragment ions (relative to the initial amount you specified at ** Molecular System**/

In the Results dialog box you select ** Type** to Reactant (blue arrow),

You continue in an analogous manner setting ** Item** to propyl radical, and check Concentration in the

The next step is to ask for the internal energy distribution curves for the molecular ion. To do so, first set ** Type** to Reactant,

Here you set ** Graph Type** to Int. Energy Distribution (red arrow), and set

You set ** Graph Type** to "Custom",

You should save it by clicking on the icon (blue arrow above) or by clicking on ** File/Save** or

Next you can prompt your computer to do the actual calculation, by clicking on ** Calculate** (green arrow).

Calculation takes a few seconds only, you can monitor progress by the blue bar at the bottom right corner. When the calculations are finished, you will get the results in the main window:

You can arrange them as in other Windows applications. The results show a fairly low survival yield (0.277) and a high effective temperature (2150 K), which is mainly the result of the high collision energy. There are only few collisions (1.24 on average). The concentrations of the molecular ion, propene loss and propyl radical loss are 1.34%, 3.42% and 0.0782%. These are all very small numbers – which indicates that most of the ions decompose either in the ion source or during flight through the 1^{st} quadrupole. Those information can be found in the Calculation Result child window:

The first Figure shows the internal energy distribution of ions in the ion source (i.e. at 1000 K, as defined):

The next Figure shows the internal energy distribution of ions before the collision cell:

This indicates that most ions above ca. 1.5 eV internal energy decomposed during mass analysis (in accordance with the low ion yields) and only low internal energy ions enter the collision cell. The next Figure shows the internal energy distribution at the end of the collision cell:

It shows a higher energy tail in the energy distribution curve, a consequence of collisional activation. (Note that ions which get to internal energy levels above ca. 2 eV decompose so fast, that they will not be apparent in this energy diagram). The last Figure shows the mean internal energy of the molecular ions as they move through the mass spectrometer:

If you want to copy the diagrams you have to click ** Edit**/

.

**How to use MassKinetics as a simple RRKM program**

Here we will show you in detail how to use the MassKinetics as a simple RRKM program. In this page various MassKinetics window names and menu items are printed ** red italic bold**; parameters to be selected by

After you create a new project click on the ** Setup** menu to define your experiment. This brings up a dialog box and proceed to the

Select the ** Molecules** tab and set the

Select the ** Results** tab and select

A new dialog will appear, then press the OK Button:

Now you have finished the ** Setup**, so you should accept it by clicking

If you want to copy the diagrams you have to click ** Edit**/

- How to calculate thermal energy distribution and average thermal energy
- Load the vibrational frequencies of the molecule (
*Molecular System**,*tab**Molecules***,*column)**Freq. Model** - Set the
to Thermal at 450K.__Initial Internal Energy__ - Set the
to 450K. Note that, this value does not influence the calculation result.__Initial Kinetic Energy__ - Uncheck the
(__Radiative Energy Transfer (RET) is considered__Tab) and*Radiation*(__Consider Collisions__Tab)*Collisions* - Set
:*Numerical Parameters*to 10 eV and__Maximum Internal Energy__to 300.__Number of Energy bins__ - Add a new 2D Graph (
tab) and set*Results*to 'Int. Energy Distribution' and set__Graph Type__to "Time" "equals", and click/type in "0"__Show Internal Energy Distribution when__ - Calculate the Thermal Energy Distribution:
- How to calculate average thermal energy as a function of temperature
- Set the MassKinetics project to calculate average thermal energy on the basis of previous Tip.
- Set the
to '1D Scan'.and__Calculation Type__to 10 (__Number of Steps__Tab):*Calculation* - Press the
button and a new dialog will appear:__Add__ - Set the
to 'Reactant',__Type__to 'Reactant',__Item__to 'Initial Internal Energy'.,__Sub-type1__to 'Temperature',__Parameter__to Linear,__Scan Function__300, and__Start Value__to 500__End Value__ - Add a new 2D Graph (
tab) and set*Results*to 'Custom',__Graph Type__to "Avg. Internal Energy",__X Axis__to 1D Scanning Parameter.__Y Axis__ - Calculate the Average Thermal Energy Distribution: as a function of temperature
- How to model on-resonance excitation experiment on FT-ICR-MS (Coming soon...)
- How to calculate a breakdown curve (Coming soon...)
- How to scan a parameter (Coming soon...)
- How to shorten the calculation time (Coming soon...)

.

How to calculate thermal energy distribution and average thermal energy

Here we will show you how to calculate thermal energy distribution using MassKinetics program.

Calculating the thermal energy distribution of Leucine Enkepahin at 450K

If you wish to calculate the average thermal internal energy, check the 'Average Internal Energy' parameter to calculate (** Results** tab,

Leucine Enkephalin:

----------------------

Avg. Internal Energy = 2.04

.

How to calculate average thermal energy as a function of temperature

Here we will show you how to calculate average thermal energy as a function of temperature using MassKinetics program:

Calculations presented in literature can be downloaded from this page, allowing further calculations or tests on those system to be performed by the interested reader.

Non-profit application of data (e.g. vibrational frequencies, MassKinetics project files) is allowed provided that this web page and the corresponding scientific article is cited.

- Modeling the kinetic method in case of salt clusters ( L. Wua, J. W. Denault, R.G. Cooks, L. Drahos and K. Vékey, Alkali Halide Cluster Dissociation Examined by the Kinetic Method: Heterolytic Bond Dissociation Energies, Effective Temperatures and Entropic Effects,
*J. Am. Soc. Mass Spectrom*,**13**, 1386-1393 (2002) ) - Modeling the effect of collisional cooling using different collision gases (Z. Takáts, L. Drahos, G. Schlosser and K. Vékey, Feasibility of Formation of Hot Ions in Electrospray,
*Anal. Chem, 2002; 74(24); 6427-6429*) - Theoretical calculation of isotope effects, kinetic energy release and effective temperatures for alkylamines (László Drahos, Judit Sztáray and Károly Vékey,
*International Journal of Mass Spectrometry*,**225**233–248 (2003) )

.

Modeling CID fragmentation of NaClRb^{+} cluster

The details of this example can be found in the following article: L. Wua, J. W. Denault, R.G. Cooks, L. Drahos and K. Vékey, *J. Am. Soc. Mass Spectrom*, **13**, 1386-1393 (2002)

Calculated (B3-LYP/SDD basis set) vibrational frequencies (cm^{-1}) of [Na-Cl-Rb]^{+}: 56.6447, 56.6456, 133.5272, 324.7957.

Click here to download this MassKinetics frequency file.

**Fig. 3a:**MassKinetic calculated survival yield vs. collision efficiency curve of [Na-Cl-Rb]^{+} under single collision conditions.

**Fig. 3b: **MassKinetic calculated effective temperature T_{eff} vs. collision efficiency curve of [Na-Cl-Rb]^{+} under single collision conditions.

Click here to download this MassKinetics project file.

**Fig. 4a:** MassKinetic calculated survival yield vs. collision gas pressure (Pa) graph.

**Fig. 3b: **MassKinetic calculated effective temperature T_{eff} vs. collision gas pressure graph.

.

Modeling collisional cooling of p-methoxy-benyzlpyridinium ion colliding with Ar, N_{2} and isobutane gases

The details of this example can be found in the following article: (Z. Takáts, L. Drahos, G. Schlosser and K. Vékey, Is Formation of Hot Ions Feasible in Electrospray?, *Anal. Chem.* in press

Calculated (B3-LYP/6-31G(d,p)) vibrational frequencies (cm^{-1}) of p-methoxy-benyzlpyridinium ion: click here to download this MassKinetics frequency file.

Collisional cooling can be modeled reasonably well assuming long-lived collision complexes. In such a case the total energy of the two collision partners (the internal energy of the two partners and their relative rotational and translational energy) is distributed statistically between the various degrees of freedom. This process has been studied by MassKinetics model calculations. Preliminary results are shown in this figure illustrating the change of mean internal energy as a function of the number of collisions. Calculations were performed for p-methoxy-benyzlpyridinium ion colliding with Ar, N_{2} and isobutane collision gases. The model calculations clearly show, that isobutane is the best cooling medium, and that the difference between Ar and N_{2} is much less than that between N_{2} and isobutane. The cooling rates shown here. agree very well with the experimentally observed difference between these curtain gases.

The corresponding MassKinetics project file will be available when MassKinetics Scientific version is released.

.

**Modeling kinetic isotope effect
(KIE), effective temperature (T _{eff}) and kinetic energy release (KER)
of selected protonated alkylamine dimers**

**Welcome!**

We would like to give you a short introduction
to the modeling of the dissociation of protonated alkylamine dimers.

Various properties of the selected systems, such as kinetic
isotope effect, effective temperature and kinetic energy release can be
calculated using the following known parameters:

·
experimental setup (instrumental setup, lengths, source
temperature, acceleration voltages)

·
reaction enthalpy, vibrational frequencies for reactants and
products, preexponential factor for defining the transitional state

These
parameters can be found in the first window of each MassKintetics project file.

The
details of these calculations, the summarized results for all the tested system
and the conclusions can be found in the following article:

L. Drahos, J. Sztáray and K. Vékey *Int.
J. Mass Spectrom.*, **225** 233–248 (2003)

Also one can find excellent references for the kinetic method
that was used to get the interested data from the ion ratios and also for the
KER.

The theoretical background of the MassKinetics program can be
found in the following article:

L.
Drahos and K. Vékey* J. Mass Spectrom.*, **36**, 237-263 (2001)

**The types of calculations presented here:**

**1.
****Modeling KIE and T _{eff} **

**2.
****Modeling KER with calculating internal energy partitioning
and calculating the kinetics energy release distributions for the product ions**

**3.
****Modeling energy distributions: calculating the
internal energy distributions of the fragmenting parent ions and of the product
ions at different places.**

The required data for each of these
calculations as well as the parameters, which have been used in the modeling
can be found in the first page of the MassKinetics project file.

Two types of experiments were
modeled: using the high-pressure ion source (VG), and using the low-pressure
ion source (JEOL). One can find the MassKinetics project files for both
systems.

Also there were 11 protonated
alkylamine systems, which were modeled and presented in the referred article.
We would like to present here two systems of those: the smallest one and the
biggest one that is the protonated methyl-amin-methyld3-amin and the protonated
dietil-amin-dietil-d2-amin system. As for the example of the distributions
calculations we only dealt with the first, smallest system, so that is
presented here too.

**1. Modeling KIE and T _{eff} **

The kinetic isotope effect and the effective temperature can
be calculated of the interested system without calculating the internal energy
partitioning between the corresponding products. This means that only the
molecular ion and the two possible fragment ions are considered in the
modeling.

MassKinetics
project file for the *protonated methyl-amin-methyld3-amin* system using *high-pressure
ion source*:

Click here to download this
MassKinetics project file.

and
using *low-pressure ion source*:

Click here to
download this MassKinetics project file.

MassKinetics
project file for the *protonated diethyl-amin-diethyld2-amin* system using
*high-pressure ion source*:

Click here to
download this MassKinetics project file.

and
using *low-pressure ion source*:

Click here to
download this MassKinetics project file.

**2.
Modeling KER with calculating internal energy partitioning**

Calculating the kinetic energy release (KER) it is required
to calculate the internal energy partitioning over the products. It can be
selected in the *Molecular System/General *window in the MassKinetics
project file. Because calculating the internal energy partitioning involves the
neutral products also, one has to make a few changes comparing to the upper
project files. The *Reaction Scheme* should include the two possible
neutral products and these have to be considered in the *Reactions* window
too. Also the frequency model of the fragment ions has to be loaded in the M*olecular
System/Molecules* window and neutral products have to be loaded in the M*olecular
System/Reactions* window. The rest of the project file is very similar to
the upper ones.

*protonated methyl-amin-methyld3-amin* system using *high-pressure
ion source*:

Click here to
download this MassKinetics project file.

and
using *low-pressure ion source*:

Click here to
download this MassKinetics project file.

*protonated diethyl-amin-diethyld2-amin* system using
*high-pressure ion source*:

Click here to
download this MassKinetics project file.

and
using *low-pressure ion source*:

Click here to
download this MassKinetics project file.

And of course one can calculate the KER distribution for the
fragment ions. In order to do that you have to go to the *Results/Reaction (M**®**X)* window and select the 2D curve for
KER distribution. Here is an example for M*®*A dissociation.

Click here to
download this MassKinetics project file.

**3.
Modeling energy distributions**

Throughout
this section the low pressure ion source (JEOL instrument) setup will be used.

a,
Thermal energy distributions of the molecular ion

First let’s calculate the thermal internal energy
distributions for the molecular ions at selected temperature.

The temperature can be given at the *Molecular System/Molecules*
window by setting the internal energy of the molecular ion. The 2D curve has to
be selected at *Result/Reactant/Molecular Ion*. The presented project file
calculates the IED at 450K (internal energy of the molecular ion).

Click here to
download this MassKinetics project file.

b,
Internal energy distributions of the fragmenting ions at various place of the
mass spectrometer

In the referred article it is shown, that the molecular ions
can dissociate through two channels:
either the deuterated or the non-deuterated product ion can be formed.

It is interesting to check the difference in the internal
energy distributions of the two possible product ions.

MassKinetics project file for the *protonated methyld3-amin*
product ion using *low-pressure ion source*:

Click here to
download this MassKinetics project file.

MassKinetics
project file for the *protonated methyl-amin *product ion using *low-pressure
ion source*:

Click here to download
this MassKinetics project file.

Since there is only a minor difference in the distributions
of the two product ions, we decided to deal only with one of the two product
ions during the modeling of the energy distributions of the ions.

To set
the place where the energy distributions should be calculated it has to be
defined when the 2D curves are being selected. Here are three examples:

1.
Ions reaching the field free flight (FFR): this is right before the third
region

Click here to
download this MassKinetics project file.

2.
Ions leaving the field free flight (FFR): this is right after the third region

Click here to
download this MassKinetics project file.

3. Ions fragmenting in the field free region: in order to get
this distribution the difference between the first two distributions has to be
taken, that is the ions leaving the FFR and the ions reaching the FFR. So you
really don’t need a project file for doing this. J

**Hope you enjoy it!**

If you have any question or comment regarding the calculations or anything else, please don’t hesitate to ask us: szj@unc.edu or masskinetics@ttk.mta.hu

If you wish to include your own example here, please send it to masskinetics@ttk.mta.hu

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MassKinetics ( 2.1.2.696)

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